best sights 2 days in tokyo with kids

We are travelling to Japan in June, 2A & 2 C. We have purchased a 7 Day JR pass, travelling to Kyoto for 3 nts, 1 nt Miyajima, then tokyo for 3 nts. We have 2 full days available for sightseeing in tokyo with our 2 children 11 & 9. Is it better to leave a day trip to Nikko for another time?

If it is the first time in Japan you should stay in Tokyo, after going to Kyoto, Miyajime, you will be exhauted.
Let's go to akihabara, shibuya dogenzaka, tsukiji market, toy shops in ginza or ueno, why not a play ground to see or pratice baseball naywhere in tokyo. You can also go for a travel on the sumida river with the "sea buses", you can also go to asakusa to see old fashion streets and shops and the senso-ji with all its shops and usually festival